convert_to_fstWig: Convert to fstwig

View source: R/utils_format_conversion.R

convert_to_fstWigR Documentation

Convert to fstwig

Description

Will split files by chromosome for faster loading for now. This feature might change in the future!

Usage

convert_to_fstWig(
  df,
  in_files = filepath(df, "pshifted"),
  out_dir = file.path(libFolder(df), "fstwig"),
  split.by.strand = TRUE,
  split.by.readlength = FALSE,
  seq_info = seqinfo(df),
  weight = "score",
  is_pre_collapsed = FALSE,
  verbose = TRUE
)

Arguments

df

an ORFik experiment, or NULL is allowed if both in_files and out_dir is specified manually.

in_files

paths to input files, default pshifted files: filepath(df, "pshifted") in ofst format

out_dir

paths to output files, default file.path(libFolder(df), "bigwig").

split.by.strand

logical, default TRUE, split into forward and reverse strand RleList inside covRle object.

split.by.readlength

logical, default FALSE, split into files for each readlength, defined by readWidths(x) for each file.

seq_info

SeqInfo object, default seqinfo(findFa(df))

weight

integer, numeric or single length character. Default "score". Use score column in loaded in_files.

is_pre_collapsed

logical, default FALSE. Have you already collapsed reads with collapse.by.scores, so each positions is only in 1 GRanges object with a score column per readlength? Set to TRUE, only if you are sure, will give a speedup.

verbose

logical, default TRUE, message about library output status.

Value

invisible(NULL), files saved to disc


Roleren/ORFik documentation built on Nov. 13, 2024, 10 p.m.